Regulation of Gene Expression

CAMPBELL BIOLOGY IN FOCUS

Urry • Cain • Wasserman • Minorsky • Jackson • Reece

15Regulation of Gene Expression

鄭先祐 (Ayo) 教授國立臺南大學生態科學與技術學系

Ayo website: http://myweb.nutn.edu.tw/~hycheng/

Overview: Differential Expression of Genes

Prokaryotes and eukaryotes alter gene expression in response to their changing environment.

Multicellular eukaryotes also develop and maintain multiple cell types.

Gene expression is often regulated at the transcription stage, but control at other stages is important, too.

Figure 15.1

Concept 15.1: Bacteria often respond to environmental change by regulating transcription

Natural selection has favored bacteria that produce only the gene products needed by the cell.

A cell can regulate the production of enzymes by feedback inhibition or by gene regulation.

Gene expression in bacteria is controlled by a mechanism described as the operon model.

Figure 15.2

Regulationof geneexpression

Precursor

trpE gene

(a) Regulation of enzyme activity

Feedbackinhibition

Enzyme 1

Enzyme 2

Enzyme 3

Tryptophan

(b) Regulation of enzyme production

trpD gene

trpC gene

trpB gene

trpA gene

Operons: The Basic Concept

A group of functionally related genes can be coordinately controlled by a single “on-off switch”

The regulatory “switch” is a segment of DNA called an operator usually positioned within the promoter.

An operon is the entire stretch of DNA that includes the operator, the promoter, and the genes that they control.

The operon can be switched off by a protein repressor.

The repressor prevents gene transcription by binding to the operator and blocking RNA polymerase.

The repressor is the product of a separate regulatory gene.

The repressor can be in an active or inactive form, depending on the presence of other molecules.

A co-repressor is a molecule that cooperates with a repressor protein to switch an operon off

For example, E. coli can synthesize the amino acid tryptophan.

By default the trp operon is on and the genes for tryptophan synthesis are transcribed.

When tryptophan is present, it binds to the trp repressor protein, which then turns the operon off.

The repressor is active only in the presence of its corepressor tryptophan; thus the trp operon is turned off (repressed) if tryptophan levels are high.

Figure 15.3a

(a) Tryptophan absent, repressor inactive, operon on

Polypeptide subunits that make upenzymes for tryptophan synthesis

Protein

Inactiverepressor

mRNA

5

3

E D C B A

Promoter

DNA

Regulatorygene

RNApolymerase

Promoter

trp operon

Genes of operon

OperatorStart codon Stop codon

mRNA 5

trpE trpD trpC trpB trpAtrpR

Figure 15.3b

DNA

mRNA

Protein Activerepressor

No RNAmade

Tryptophan(corepressor)

(b) Tryptophan present, repressor active, operon off

Repressible and Inducible Operons: Two Types of Negative Gene Regulation

A repressible operon is one that is usually on; binding of a repressor to the operator shuts off transcription.

The trp operon is a repressible operon.

An inducible operon is one that is usually off; a molecule called an inducer inactivates the repressor and turns on transcription.

The lac operon is an inducible operon and contains genes that code for enzymes used in the hydrolysis and metabolism of lactose.

By itself, the lac repressor is active and switches the lac operon off.

A molecule called an inducer inactivates the repressor to turn the lac operon on.

For the lac operon, the inducer is allolactose, formed from lactose that enters the cell.

Enzymes of the lactose pathway are called inducible enzymes.

Analogously, the enzymes for tryptophan synthesis are said to be repressible enzymes.

Figure 15.4a

DNA

PromoterOperator

Regulatorygene

NoRNAmade

IacZlacI

mRNA RNApolymerase

3

5

ActiverepressorProtein

(a) Lactose absent, repressor active, operon off

Figure 15.4b

IacZ IacY IacAIacI

DNA lac operon

Permease Transacetylase-Galactosidase

mRNA

Protein

RNA polymerase

mRNA 53

5

Inactiverepressor

Allolactose(inducer)

(b) Lactose present, repressor inactive, operon on

Inducible enzymes usually function in catabolic (分解代謝的 ) pathways; their synthesis is induced by a chemical signal.

Repressible enzymes usually function in anabolic (合成代謝的 ) pathways; their synthesis is repressed by high levels of the end product.

Regulation of the trp and lac operons involves negative control of genes because operons are switched off by the active form of the repressor.

Positive Gene Regulation

E. coli will preferentially use glucose when it is present in the environment.

When glucose is scarce, CAP (catabolite activator protein) acts as an activator of transcription.

CAP is activated by binding with cyclic AMP (cAMP).

Activated CAP attaches to the promoter of the lac operon and increases the affinity of RNA polymerase, thus accelerating transcription.

When glucose levels increase, CAP detaches from the lac operon, and transcription proceeds at a very low rate, even if lactose is present.

CAP helps regulate other operons that encode enzymes used in catabolic pathways.

Figure 15.5

DNA

Promoter

Operator

IacZlacI

CAP-binding site

cAMP

InactiveCAP

ActiveCAP

RNApolymerasebinds andtranscribes

Allolactose

Inactive lacrepressor

(a) Lactose present, glucose scarce (cAMP level high):

Promoter

abundant lac mRNA synthesized

DNA

Operator

IacZlacI

CAP-binding siteRNApolymerase lesslikely to bind

(b) Lactose present, glucose present (cAMP level low):little lac mRNA synthesized

InactiveCAP


Figure 15.5a

DNA

Promoter

IacZlacI

OperatorRNApolymerasebinds andtranscribes

ActiveCAP

InactiveCAP

Allolactose


CAP-binding site

cAMP

(a) Lactose present, glucose scarce (cAMP level high):abundant lac mRNA synthesized

Figure 15.5b

Promoter

DNA

Operator

IacZlacI

CAP-binding site

InactiveCAP Inactive lac

repressor

RNApolymerase lesslikely to bind

little lac mRNA synthesized(b) Lactose present, glucose present (cAMP level low):

Concept 15.2: Eukaryotic gene expression is regulated at many stages

All organisms must regulate which genes are expressed at any given time.

In multicellular organisms regulation of gene expression is essential for cell specialization.

Differential Gene Expression

Almost all the cells in an organism are genetically identical.

Differences between cell types result from differential gene expression, the expression of different genes by cells with the same genome.

Abnormalities in gene expression can lead to diseases, including cancer.

Gene expression is regulated at many stages.

Figure 15.6aSignal

NUCLEUSChromatin

Chromatin modification:DNA unpacking involvinghistone acetylation and

DNA demethylationDNA

Gene

RNA Exon

Gene availablefor transcription

Transcription

Primary transcript

IntronRNA processing

TailmRNA in nucleus

Transport to cytoplasm

Cap

CYTOPLASM

Figure 15.6b

CYTOPLASM

mRNA in cytoplasm

TranslationDegradationof mRNA

Polypeptide

Protein processing, suchas cleavage and

chemical modification

Active protein

Transport to cellulardestination

Degradationof protein

Cellular function(such as enzymaticactivity, structural support)

In all organisms, a common control point for gene expression is at transcription.

The greater complexity of eukaryotic cell structure and function provides opportunities for regulating gene expression at many additional stages.

Regulation of Chromatin Structure

The structural organization of chromatin packs DNA into a compact form and also helps regulate gene expression in several ways

The location of a gene promoter relative to nucleosomes and scaffold (鷹架 ) or lamina (薄板 ) attachment sites can influence gene transcription.

Genes within highly condensed heterochromatin are usually not expressed.

Chemical modifications to histone proteins and DNA can influence chromatin structure and gene expression.

Histone Modifications and DNA Methylation

In histone acetylation, acetyl groups are attached to positively charged lysines (離氨基酸 ) in histone tails.

This generally loosens chromatin structure, promoting the initiation of transcription.

The addition of methyl groups (methylation) can condense chromatin and lead to reduced transcription.

Figure 15.7

Nucleosome

Unacetylated histones Acetylated histones

Histonetails

DNA methylation is the addition of methyl groups to certain bases in DNA, usually cytosine.

Individual genes are usually more heavily methylated in cells where they are not expressed

Once methylated, genes usually remain so through successive cell divisions

After replication, enzymes methylate the correct daughter strand so that the methylation pattern is inherited.

Epigenetic Inheritance ( 表觀遺傳學 )

Though chromatin modifications do not alter DNA sequence, they may be passed to future generations of cells

The inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence is called epigenetic inheritance ( 表觀遺傳學 ).

Epigenetic modifications can be reversed, unlike mutations in DNA sequence.

Regulation of Transcription Initiation

Chromatin-modifying enzymes provide initial control of gene expression by making a region of DNA either more or less able to bind the transcription machinery.

Organization of a Typical Eukaryotic Gene

Associated with most eukaryotic genes are multiple control elements, segments of noncoding DNA that serve as binding sites for transcription factors that help regulate transcription.

Control elements and the transcription factors they bind are critical for the precise regulation of gene expression in different cell types.

Animation: mRNA DegradationRight click slide / Select play

Figure 15.8b-1

Proximalcontrol

elementsTranscription

start site

Exon Intron Exon

Promoter

Intron Exon

Poly-A signalsequence

DNA

Exon = 編碼順序

Figure 15.8b-2

Proximalcontrol


start site

Promoter


DNA

Transcription

Exon Intron IntronExon Exon

Poly-Asignal

Primary RNAtranscript(pre-mRNA)

5Cleaved 3end ofprimarytranscript

Exon Intron Exon Intron Exon

Figure 15.8b-3

Proximalcontrol


start site

Promoter


DNA

Transcription

Exon Intron IntronExon Exon

Poly-Asignal

Primary RNAtranscript(pre-mRNA)

5Cleaved 3end ofprimarytranscriptIntron RNA

mRNA

RNA processing

Coding segment

3

5 5 3Cap UTRStart

codonStop

codon UTR Poly-Atail

G P P P AAAAAA

Exon Intron Exon Intron Exon

The Roles of Transcription Factors

To initiate transcription, eukaryotic RNA polymerase requires the assistance of proteins called transcription factors.

General transcription factors are essential for the transcription of all protein-coding genes.

In eukaryotes, high levels of transcription of particular genes depend on interaction between control elements and specific transcription factors.

Proximal control elements are located close to the promoter.

Distal control elements, groupings of which are called enhancers, may be far away from a gene or even located in an intron (內含子 )

Enhancers and Specific Transcription Factors

An activator is a protein that binds to an enhancer and stimulates transcription of a gene.

Activators have two domains, one that binds DNA and a second that activates transcription.

Bound activators facilitate a sequence of protein-protein interactions that result in transcription of a given gene.

Figure 15.9

Activationdomain

DNA

DNA-bindingdomain

MyoD, a transcription activator. The MyoD protein is made up of two subunits (purple and salmon 淺橙色 ) with extensive regions of α helix.

Bound activators are brought into contact with a group of mediator proteins through DNA bending.

The mediator proteins in turn interact with proteins at the promoter.

These protein-protein interactions help to assemble and position the initiation complex on the promoter.

Animation: Transcription InitiationRight click slide / Select play

Figure 15.UN01

Chromatin modification

Transcription

RNA processing

TranslationmRNAdegradation

Proteinprocessing

and degradation

Figure 15.10-1

DNA

EnhancerDistal controlelement

Activators PromoterGene

TATA box

Figure 15.10-2

DNA



TATA box

DNA-bendingprotein

Group of mediator proteins

General transcriptionfactors

Figure 15.10-3

DNA



TATA box

DNA-bendingprotein

Group of mediator proteins

General transcriptionfactors

RNApolymerase II

RNApolymerase II

RNA synthesisTranscriptioninitiation complex

Some transcription factors function as repressors, inhibiting expression of a particular gene by a variety of methods.

Some activators and repressors act indirectly by influencing chromatin structure to promote or silence transcription.

Combinatorial Control of Gene Activation

A particular combination of control elements can activate transcription only when the appropriate activator proteins are present.

Figure 15.11Albumin gene

Crystallin gene

Promoter

Promoter

(b) LENS CELL NUCLEUS

Availableactivators

Albumin genenot expressed

Crystallin geneexpressed

Crystallin genenot expressed

Albumin geneexpressed

Availableactivators

(a) LIVER CELL NUCLEUS

Controlelements

Enhancer

Enhancer

Coordinately Controlled Genes in Eukaryotes

Unlike the genes of a prokaryotic operon, each of the co-expressed eukaryotic genes has a promoter and control elements

These genes can be scattered over different chromosomes, but each has the same combination of control elements

Copies of the activators recognize specific control elements and promote simultaneous transcription of the genes

Mechanisms of Post-Transcriptional Regulation

Transcription alone does not account for gene expression

Regulatory mechanisms can operate at various stages after transcription

Such mechanisms allow a cell to fine-tune gene expression rapidly in response to environmental changes

RNA Processing

In alternative RNA splicing, different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns

Animation: RNA ProcessingRight click slide / Select play

Figure 15.UN02


Transcription

RNA processing


Proteinprocessing

and degradation

Figure 15.12

DNA

PrimaryRNAtranscript

mRNA or

Exons

Troponin T gene

RNA splicing

1 2 3 4 5

1 2 3 5 1 2 4 5

1 2 3 4 5

mRNA Degradation

The life span of mRNA molecules in the cytoplasm is important in determining the pattern of protein synthesis in a cell

Eukaryotic mRNA generally survives longer than prokaryotic mRNA

Nucleotide sequences that influence the life span of mRNA in eukaryotes reside in the untranslated region (UTR) at the 3 end of the molecule

Initiation of Translation

The initiation of translation of selected mRNAs can be blocked by regulatory proteins that bind to sequences or structures of the mRNA

Alternatively, translation of all mRNAs in a cell may be regulated simultaneously

For example, translation initiation factors are simultaneously activated in an egg following fertilization

Protein Processing and Degradation

After translation, various types of protein processing, including cleavage and chemical modification, are subject to control

The length of time each protein functions in a cell is regulated by means of selective degradation

To mark a particular protein for destruction, the cell commonly attaches molecules of ubiquitin to the protein, which triggers its destruction

Concept 15.3: Noncoding RNAs play multiple roles in controlling gene expression

Only a small fraction of DNA encodes proteins, and a very small fraction of the non-protein-coding DNA consists of genes for RNA such as rRNA and tRNA

A significant amount of the genome may be transcribed into noncoding RNAs (ncRNAs)

Noncoding RNAs regulate gene expression at several points

Effects on mRNAs by MicroRNAs and Small Interfering RNAs

MicroRNAs (miRNAs) are small single-stranded RNA molecules that can bind to complementary mRNA sequences

These can degrade the mRNA or block its translation

Figure 15.UN03


Transcription

RNA processing


Proteinprocessing

and degradation

Figure 15.13miRNA

miRNA-proteincomplex

Translation blockedmRNA degraded

The miRNA bindsto a target mRNA.

1

If bases are completely complementary, mRNA is degraded.If match is less than complete, translation is blocked.

2

Another class of small RNAs are called small interfering RNAs (siRNAs)

siRNAs and miRNAs are similar but form from different RNA precursors

The phenomenon of inhibition of gene expression by siRNAs is called RNA interference (RNAi)

Chromatin Remodeling and Effects on Transcription by ncRNAs

In some yeasts RNA produced from centromeric DNA is copied into double-stranded RNA and then processed into siRNAs

The siRNAs, together with a complex of proteins, act as a homing device to target transcripts being made from centromeric sequences

Proteins in the complex then recruit enzymes that modify the chromatin to form the highly condensed heterochromatin found at the centromere

A class of small ncRNAs called piwi-associated RNAs (piRNAs) also induce formation of heterochromatin

They block expression of transposons, parasitic DNA elements in the genome

The role of ncRNAs adds to the complexity of the processes involved in regulation of gene expression

Concept 15.4: Researchers can monitor expression of specific genes

Cells of a given multicellular organism differ from each other because they express different genes from an identical genome

The most straightforward way to discover which genes are expressed by cells of interest is to identify the mRNAs being made

Studying the Expression of Single Genes

We can detect mRNA in a cell using nucleic acid hybridization, the base pairing of a strand of nucleic acid to its complementary sequence

The complementary molecule in this case is a short single-stranded DNA or RNA called a nucleic acid probe

Each probe is labeled with a fluorescent tag to allow visualization

The technique allows us to see the mRNA in place (in situ) in the intact organism and is thus called in situ hybridization

Figure 15.14

50 m

Another widely used method for comparing the amounts of specific mRNAs in several different samples is reverse transcriptase–polymerase chain reaction (RT-PCR)

RT-PCR turns sample sets of mRNAs into double- stranded DNAs with the corresponding sequences

RT-PCR relies on the activity of reverse transcriptase, which can synthesize a DNA copy of an mRNA, called a complementary DNA (cDNA)

Once the cDNA is produced, PCR is used to make many copies of the sequence of interest, using primers specific to that sequence

Figure 15.15-1

Test tube containingreverse transcriptaseand mRNA

DNA in nucleus

mRNAs incytoplasm

1

Figure 15.15-2


DNA in nucleus

mRNAs incytoplasm

Reverse transcriptasemakes the firstDNA strand.

Reversetranscriptase

mRNAPoly-A tail

DNAstrand

Primer

53

35

A A A A A AT

1

2

T T T T

Figure 15.15-3


DNA in nucleus

mRNAs incytoplasm



mRNAPoly-A tail

DNAstrand

Primer

53

35

A A A A A A

1

2

mRMA is degraded.353

35

A A AT

A A A

T T T T T

T T T T

Figure 15.15-4


DNA in nucleus

mRNAs incytoplasm



mRNAPoly-A tail

DNAstrand

Primer

53

35

A A A A A A

1

2


35

A A A A A A

DNA polymerasesynthesizes thesecond strand.

DNApolymerase

53

35

4

T

T T T T T

T T T T

Figure 15.15-5


DNA in nucleus

mRNAs incytoplasm



mRNAPoly-A tail

DNAstrand

Primer

53

35

A A A A A A

1

2


35

A A A A A A

DNA polymerasesynthesizes thesecond strand.

DNApolymerase

53

35

4

53

35

cDNA

cDNA carries completecoding sequencewithout introns.

5

T

T T T T T

T T T T

Figure 15.16

mRNAs

cDNAs

Embryonic stages1

cDNA synthesis

PCR amplification

Gel electrophoresis

Results

Technique

1

2

3

Primers

-globingene

2 3 4 5 6

Studying the Expression of Groups of Genes

A major goal of biologists is to learn how genes act together to produce and maintain a functioning organism

Large groups of genes are studied by a systems approach

Such approaches allow networks of expression across a genome to be identified

Genome-wide expression studies can be carried out using DNA microarray assays

A microarray—also called a DNA chip—contains tiny amounts of many single-stranded DNA fragments affixed to the slide in a grid

mRNAs from cells of interest are isolated and made into cDNAs labeled with fluorescent molecules

cDNAs from two different samples are labeled with different fluorescent tags and tested on the same microarray

The experiment can identify subsets of genes that are being expressed differently in one sample compared to another

Figure 15.17

Genes in redwells expressedin first tissue.

Genes in greenwells expressedin second tissue.

Genes in yellowwells expressedin both tissues.

Genes in blackwells notexpressed in either tissue.

DNA microarray

84

問題與討論• Ayo NUTN website:• http://myweb.nutn.edu.tw/~hycheng/

Regulation of Gene Expression

Documents

Transcript of Regulation of Gene Expression